OBJECTIVE: To develop a computerised system that will assist the early diagnosis of fetal hypoxia and to investigate the relationship between the fetal heart rate variability and the fetal pulse oximetry recordings. DESIGN: Retrospective off-line analysis of cardiotocogram and FSpO2 recordings. SETTING: The Maternity Unit of the 2nd Department of Obstetrics and Gynaecology, Aretaieion Hospital, University of Athens. POPULATION: Sixty-one women of more than 37 weeks of gestation were monitored throughout labour. METHODS: Multiresolution wavelet analysis was applied in each 10-minute period of second stage of labour focussing on long term variability changes in different frequency ranges and statistical analysis was performed in the associated 10-minute FSpO2 recordings. Self-organising map neural network was used to categorise the different 10-minute fetal heart rate patterns and the associated 10-minute FSpO2 recordings. MAIN OUTCOME MEASURES: Umbilical artery pH of < or = 7.20 and Apgar score at 5 minutes of < or = 7 formed the inclusion criteria of the risk group. RESULTS: After using k-means clustering algorithm, the two-dimensional output layer of the self-organising map neural network was divided into three distinct clusters. All the cases that mapped in cluster 3 belonged in the risk group except one. The sensitivity of the system was 83.3% and the specificity 97.9% for the detection of risk group cases. CONCLUSIONS: A relationship between the fetal heart rate variability in different frequency ranges and the time in which FSpO2 is less than 30% was noticed. Fetal pulse oximetry seems to be an important additional source of information. Computerised analysis of the fetal heart rate monitoring and pulse oximetry recordings is a promising technique in objective intrapartum diagnosis of fetal hypoxia. Further evaluation of this technique is mandatory to evaluate its efficacy and reliability in interpreting fetal heart rate recordings.